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Yorodumi- EMDB-43483: Refined density map of gamma tubulin ring complex capped microtubule -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43483 | |||||||||
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Title | Refined density map of gamma tubulin ring complex capped microtubule | |||||||||
Map data | Refined density map for gamma tubulin ring complex capped microtubule | |||||||||
Sample |
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Keywords | Microtubule nucleation complex bound to a microtubule / CELL CYCLE | |||||||||
Function / homology | Function and homology information netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule minus-end binding / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / regulation of transepithelial transport / dorsal root ganglion development ...netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule minus-end binding / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / regulation of transepithelial transport / dorsal root ganglion development / mitotic spindle microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gamma-tubulin ring complex / morphogenesis of a polarized epithelium / Cilium Assembly / interphase microtubule organizing center / bBAF complex / Carboxyterminal post-translational modifications of tubulin / polar microtubule / postsynaptic actin cytoskeleton organization / npBAF complex / gamma-tubulin complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / meiotic spindle organization / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / GBAF complex / dense body / Formation of annular gap junctions / cytoskeleton-dependent intracellular transport / regulation of G0 to G1 transition / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / microtubule nucleation / Gap junction assembly / apical protein localization / COPI-independent Golgi-to-ER retrograde traffic / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / gamma-tubulin binding / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / non-motile cilium / Adherens junctions interactions / Assembly and cell surface presentation of NMDA receptors / tight junction / Kinesins / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / microtubule organizing center / positive regulation of T cell differentiation / apical junction complex / COPI-dependent Golgi-to-ER retrograde traffic / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / intercellular bridge / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of stem cell population maintenance / pericentriolar material / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / cytoplasmic microtubule / cell leading edge / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / mitotic sister chromatid segregation / kinesin binding / brush border / calyx of Held / microtubule-based process / negative regulation of cell differentiation / RHOH GTPase cycle / condensed nuclear chromosome / positive regulation of double-strand break repair via homologous recombination / mitotic spindle assembly / EPH-ephrin mediated repulsion of cells / single fertilization / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / spindle assembly / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / cellular response to interleukin-4 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
Authors | Aher A / Urnavicius L / Kapoor TM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the γ-tubulin ring complex-capped microtubule. Authors: Amol Aher / Linas Urnavicius / Allen Xue / Kasahun Neselu / Tarun M Kapoor / Abstract: Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules ...Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the long axis of the filament. We report that the human ~2.3 MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryogenic electron microscopy reconstructions of γ-TuRC-capped microtubule minus ends reveal the extensive intra-domain and inter-domain motions of γ-TuRC subunits that accommodate luminal bridge components and establish lateral and longitudinal interactions between γ-tubulins and α-tubulins. Our structures suggest that γ-TuRC, an inefficient nucleation template owing to its splayed conformation, can transform into a compacted cap at the microtubule minus end and set the lattice architecture of cellular microtubules. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43483.map.gz | 35.7 MB | EMDB map data format | |
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Header (meta data) | emd-43483-v30.xml emd-43483.xml | 29.6 KB 29.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43483_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_43483.png | 117.5 KB | ||
Filedesc metadata | emd-43483.cif.gz | 10.4 KB | ||
Others | emd_43483_half_map_1.map.gz emd_43483_half_map_2.map.gz | 140.9 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43483 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43483 | HTTPS FTP |
-Validation report
Summary document | emd_43483_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_43483_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_43483_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_43483_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43483 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43483 | HTTPS FTP |
-Related structure data
Related structure data | 8vrkMC 8vrjC 8vt7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43483.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Refined density map for gamma tubulin ring complex capped microtubule | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map for gamma tubulin ring complex capped microtubule
File | emd_43483_half_map_1.map | ||||||||||||
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Annotation | Half map for gamma tubulin ring complex capped microtubule | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map for gamma tubulin ring complex capped microtubule
File | emd_43483_half_map_2.map | ||||||||||||
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Annotation | Half map for gamma tubulin ring complex capped microtubule | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Gamma tubulin ring complex bound to microtubule minus end
+Supramolecule #1: Gamma tubulin ring complex bound to microtubule minus end
+Macromolecule #1: Tubulin alpha-1B chain
+Macromolecule #2: Tubulin beta-3 chain
+Macromolecule #3: TUBGCP6 protein
+Macromolecule #4: Gamma-tubulin complex component 3
+Macromolecule #5: Mitotic-spindle organizing protein 1
+Macromolecule #6: Actin, cytoplasmic 1
+Macromolecule #7: Isoform 3 of Gamma-tubulin complex component 2
+Macromolecule #8: Isoform 2 of Gamma-tubulin complex component 4
+Macromolecule #9: Gamma-tubulin complex component 5
+Macromolecule #10: Tubulin gamma-1 chain
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |